Accuracy of atomistic MD simulations depends critically on the solvent model. In this work, distributions of sodium and potassium ions around DNA in common models of water: SPC/E, TIP3P and OPC, with Joung/Cheatham (J/C) ion parameter set, as well as Li/Merz HFE (L/M HFE) ions for OPC water are compared. The results are also compared with experimental data, where available. Beyond 7 angstroms from the DNA helical axis, ion distributions have the same shape in every solvent model, independent of the DNA sequence or ion type; the distributions follow the Debye–Hückel theory beyond 16 angstroms from the axis. Ion distributions in close proximity to the DNA show clear dependence on the solvent model; for example, number of potassium ions in the minor groove of AT-tracts differs at least three-fold between the solvent models tested. In agreement with experiment, binding affinity of sodium and potassium ions to DNA is the same (to within 0.2 kBT) in every solvent model. The number of sodium ions associated with the DNA agrees quantitatively with experiment for OPC+L/M HFE solvent model, followed closely by OPC+J/C and TIP3P+J/C. The largest deviation from the experiment is seen for SPC/E+J/C solvent model. On the other hand, SPC/E+J/C shows highest consistency (67%) with experimental potassium binding sites, followed by OPC+J/C (60%). In summary, the choice of solvent model matters little for simulating diffuse atmosphere of monovalent ions around DNA, but close to the helical axis the distribution of ions becomes very sensitive to the solvent model used. There is no single "gold standard" solvent model, although OPC water + J/C ions might be an imperfect compromise. Conclusions that are robust to the choice of two different solvent models may be most trustworthy.

Similarities and differences of Na+ and K+ distributions around DNA obtained with three popular water models

ACS Spring Meeting 2021

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